[Bioc-sig-seq] short read low complexity filtering

[Hervé Pagès]

On 12/08/2010 03:03 PM, Hervé Pagès wrote:
[...]
>
>> Also, how would we generate the two output files:
>> name_low_complexity_removed.fastq and low_complexity_reads.fastq?
>
> You could try to use write.XStringSet(... , format="fastq") for this.
> Or use the IO facilities of the ShortRead package. It depends what you
> want to do with the scores.
                       ^^^^^^
I meant "with the qualities". The FASTQ format stores the qualities of
the reads too.

H.